src/mdlib/calcvir.c

   1 /*
   2  *
   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
   6  *
   7  *          GROningen MAchine for Chemical Simulations
   8  *
   9  *                        VERSION 3.2.0
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  11  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
  14
  15  * This program is free software; you can redistribute it and/or
  16  * modify it under the terms of the GNU General Public License
  17  * as published by the Free Software Foundation; either version 2
  18  * of the License, or (at your option) any later version.
  19  *
  20  * If you want to redistribute modifications, please consider that
  21  * scientific software is very special. Version control is crucial -
  22  * bugs must be traceable. We will be happy to consider code for
  23  * inclusion in the official distribution, but derived work must not
  24  * be called official GROMACS. Details are found in the README & COPYING
  25  * files - if they are missing, get the official version at www.gromacs.org.
  26  *
  27  * To help us fund GROMACS development, we humbly ask that you cite
  28  * the papers on the package - you can find them in the top README file.
  29  *
  30  * For more info, check our website at http://www.gromacs.org
  31  *
  32  * And Hey:
  33  * GROwing Monsters And Cloning Shrimps
  34  */
  35 /* This file is completely threadsafe - keep it that way! */
  36 #ifdef HAVE_CONFIG_H
  37 #include <config.h>
  38 #endif
  39
  40 #include "sysstuff.h"
  41 #include "force.h"
  42 #include "vec.h"
  43 #include "mshift.h"
  44 #include "macros.h"
  45
  46 static void dprod1(rvec vir,real x,rvec f)
  47 {
  48   vir[XX]+=x*f[XX];
  49   vir[YY]+=x*f[YY];
  50   vir[ZZ]+=x*f[ZZ];
  51 }
  52
  53 static void upd_vir(rvec vir,real dvx,real dvy,real dvz)
  54 {
  55   vir[XX]-=0.5*dvx;
  56   vir[YY]-=0.5*dvy;
  57   vir[ZZ]-=0.5*dvz;
  58 }
  59
  60 void calc_vir(FILE *log,int nxf,rvec x[],rvec f[],tensor vir,
  61               bool bScrewPBC,matrix box)
  62 {
  63   int      i,isx;
  64   double   dvxx=0,dvxy=0,dvxz=0,dvyx=0,dvyy=0,dvyz=0,dvzx=0,dvzy=0,dvzz=0;
  65
  66   for(i=0; (i<nxf); i++) {
  67     dvxx+=x[i][XX]*f[i][XX];
  68     dvxy+=x[i][XX]*f[i][YY];
  69     dvxz+=x[i][XX]*f[i][ZZ];
  70
  71     dvyx+=x[i][YY]*f[i][XX];
  72     dvyy+=x[i][YY]*f[i][YY];
  73     dvyz+=x[i][YY]*f[i][ZZ];
  74
  75     dvzx+=x[i][ZZ]*f[i][XX];
  76     dvzy+=x[i][ZZ]*f[i][YY];
  77     dvzz+=x[i][ZZ]*f[i][ZZ];
  78
  79     if (bScrewPBC) {
  80       isx = IS2X(i);
  81       /* We should correct all odd x-shifts, but the range of isx is -2 to 2 */
  82       if (isx == 1 || isx == -1) {
  83         dvyy += box[YY][YY]*f[i][YY];
  84         dvyz += box[YY][YY]*f[i][ZZ];
  85
  86         dvzy += box[ZZ][ZZ]*f[i][YY];
  87         dvzz += box[ZZ][ZZ]*f[i][ZZ];
  88       }
  89     }
  90   }
  91
  92   upd_vir(vir[XX],dvxx,dvxy,dvxz);
  93   upd_vir(vir[YY],dvyx,dvyy,dvyz);
  94   upd_vir(vir[ZZ],dvzx,dvzy,dvzz);
  95 }
  96
  97
  98 static void lo_fcv(int i0,int i1,int g0,
  99                    real x[],real f[],tensor vir,
 100                    int is[],real box[], bool bTriclinic)
 101 {
 102   int      i,i3,gg,g3,tx,ty,tz;
 103   real     xx,yy,zz;
 104   real     dvxx=0,dvxy=0,dvxz=0,dvyx=0,dvyy=0,dvyz=0,dvzx=0,dvzy=0,dvzz=0;
 105
 106   if(bTriclinic) {
 107       for(i=i0,gg=g0; (i<i1); i++,gg++) {
 108           i3=DIM*i;
 109           g3=DIM*gg;
 110           tx=is[g3+XX];
 111           ty=is[g3+YY];
 112           tz=is[g3+ZZ];
 113
 114           xx=x[i3+XX]-tx*box[XXXX]-ty*box[YYXX]-tz*box[ZZXX];
 115           dvxx+=xx*f[i3+XX];
 116           dvxy+=xx*f[i3+YY];
 117           dvxz+=xx*f[i3+ZZ];
 118
 119           yy=x[i3+YY]-ty*box[YYYY]-tz*box[ZZYY];
 120           dvyx+=yy*f[i3+XX];
 121           dvyy+=yy*f[i3+YY];
 122           dvyz+=yy*f[i3+ZZ];
 123
 124           zz=x[i3+ZZ]-tz*box[ZZZZ];
 125           dvzx+=zz*f[i3+XX];
 126           dvzy+=zz*f[i3+YY];
 127           dvzz+=zz*f[i3+ZZ];
 128       }
 129   } else {
 130       for(i=i0,gg=g0; (i<i1); i++,gg++) {
 131           i3=DIM*i;
 132           g3=DIM*gg;
 133           tx=is[g3+XX];
 134           ty=is[g3+YY];
 135           tz=is[g3+ZZ];
 136
 137           xx=x[i3+XX]-tx*box[XXXX];
 138           dvxx+=xx*f[i3+XX];
 139           dvxy+=xx*f[i3+YY];
 140           dvxz+=xx*f[i3+ZZ];
 141
 142           yy=x[i3+YY]-ty*box[YYYY];
 143           dvyx+=yy*f[i3+XX];
 144           dvyy+=yy*f[i3+YY];
 145           dvyz+=yy*f[i3+ZZ];
 146
 147           zz=x[i3+ZZ]-tz*box[ZZZZ];
 148           dvzx+=zz*f[i3+XX];
 149           dvzy+=zz*f[i3+YY];
 150           dvzz+=zz*f[i3+ZZ];
 151       }
 152   }
 153
 154   upd_vir(vir[XX],dvxx,dvxy,dvxz);
 155   upd_vir(vir[YY],dvyx,dvyy,dvyz);
 156   upd_vir(vir[ZZ],dvzx,dvzy,dvzz);
 157 }
 158
 159 static void lo_fcv2(int i0,int i1,
 160                     rvec x[],rvec f[],tensor vir,
 161                     ivec is[],matrix box, bool bTriclinic)
 162 {
 163   int      i,gg,tx,ty,tz;
 164   real     xx,yy,zz;
 165   real     dvxx=0,dvxy=0,dvxz=0,dvyx=0,dvyy=0,dvyz=0,dvzx=0,dvzy=0,dvzz=0;
 166
 167   if(bTriclinic) {
 168       for(i=i0,gg=0; (i<i1); i++,gg++) {
 169           tx=is[gg][XX];
 170           ty=is[gg][YY];
 171           tz=is[gg][ZZ];
 172
 173           xx=x[i][XX]-tx*box[XX][XX]-ty*box[YY][XX]-tz*box[ZZ][XX];
 174           dvxx+=xx*f[i][XX];
 175           dvxy+=xx*f[i][YY];
 176           dvxz+=xx*f[i][ZZ];
 177
 178           yy=x[i][YY]-ty*box[YY][YY]-tz*box[ZZ][YY];
 179           dvyx+=yy*f[i][XX];
 180           dvyy+=yy*f[i][YY];
 181           dvyz+=yy*f[i][ZZ];
 182
 183           zz=x[i][ZZ]-tz*box[ZZ][ZZ];
 184           dvzx+=zz*f[i][XX];
 185           dvzy+=zz*f[i][YY];
 186           dvzz+=zz*f[i][ZZ];
 187       }
 188   } else {
 189       for(i=i0,gg=0; (i<i1); i++,gg++) {
 190           tx=is[gg][XX];
 191           ty=is[gg][YY];
 192           tz=is[gg][ZZ];
 193
 194           xx=x[i][XX]-tx*box[XX][XX];
 195           dvxx+=xx*f[i][XX];
 196           dvxy+=xx*f[i][YY];
 197           dvxz+=xx*f[i][ZZ];
 198
 199           yy=x[i][YY]-ty*box[YY][YY];
 200           dvyx+=yy*f[i][XX];
 201           dvyy+=yy*f[i][YY];
 202           dvyz+=yy*f[i][ZZ];
 203
 204           zz=x[i][ZZ]-tz*box[ZZ][ZZ];
 205           dvzx+=zz*f[i][XX];
 206           dvzy+=zz*f[i][YY];
 207           dvzz+=zz*f[i][ZZ];
 208       }
 209   }
 210
 211   upd_vir(vir[XX],dvxx,dvxy,dvxz);
 212   upd_vir(vir[YY],dvyx,dvyy,dvyz);
 213   upd_vir(vir[ZZ],dvzx,dvzy,dvzz);
 214 }
 215
 216 void f_calc_vir(FILE *log,int i0,int i1,rvec x[],rvec f[],tensor vir,
 217                 t_graph *g,matrix box)
 218 {
 219   int start,end;
 220
 221   if (g && (g->nnodes > 0)) {
 222     /* Calculate virial for bonded forces only when they belong to
 223      * this node.
 224      */
 225     start = max(i0,g->start);
 226     end   = min(i1,g->end+1);
 227 #ifdef SAFE
 228     lo_fcv2(start,end,x,f,vir,g->ishift,box,TRICLINIC(box));
 229 #else
 230     lo_fcv(start,end,0,x[0],f[0],vir,g->ishift[0],box[0],TRICLINIC(box));
 231 #endif
 232
 233     /* If not all atoms are bonded, calculate their virial contribution
 234      * anyway, without shifting back their coordinates.
 235      * Note the nifty pointer arithmetic...
 236      */
 237     if (start > i0)
 238       calc_vir(log,start-i0,x + i0,f + i0,vir,FALSE,box);
 239     if (end < i1)
 240       calc_vir(log,i1-end,x + end,f + end,vir,FALSE,box);
 241   }
 242   else
 243     calc_vir(log,i1-i0,x + i0,f + i0,vir,FALSE,box);
 244 }